They *did* just invade Romulan space and STEAL something didn't they? And destroy the career (if she and possibly others wern't executed) of an innocent woman, right?"

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The sentiment in the cold-war (and certainly the concept of the neutral zone was a cold-war one) was that dueling espionage was far preferable to full-out conflict, which it was, otherwise we'd be glowing by now from nuclear fallout.

A lot of interesting responses for episodes I had mercifully forgotten; I suppose I asked for it! I still think abandoning their own children just to cover for their personal discomfort over the situation must rank pretty high on the personal wrongness scale! Another one that particularly bothered me was an Enterprise episode in which the Dr's blob of something or other was cloned into a short lived copy of the engineer.

Several people have mentioned this episode but sorry I have the worst memory for titles. What was that one about?

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Good question. The only time I ever saw it was when it premiered. I don't remember anything about it, other than I seem to think favorably about it. Of course, it's possible that was due solely to Billingsley performance and not the content.

Since we're talking ethically wrong, DS9 takes all the top places, be it all the episodes that very strongly imply that you have to appeal to a stronger power for literal salvation (Sacrifice of Angels comes to mind) or deliberately shady episodes like In the Pale Moonlight.

In the Pale Moonlight is a very good episode, but its ethics are wrong on more than the "means justify the ends" angle they went with: said "ends" aren't so noble to begin with.
I mean, sure, as viewers, we can agree that Romulan involvement in the war was in everyone's interests and Sisko is clearly convinced of it as well... but if you examine it critically, is it so obvious? And even if it is, who's Sisko to forego the Romulan right to self-determination?

Also have to go with "Dear Doctor." A truly repellent episode that uses racist pseudoscience to justify passive genocide. That's the episode that needs to be stricken from canon.

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Several people have mentioned this episode but sorry I have the worst memory for titles. What was that one about?

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a first season ENT episode where the crew comes to a planet with two races, the Valakians and the Menk, living together. One of the races is dying of a plague, and even though Phlox discovers a cure, he and Archer agree to withhold it on the basis of Phlox' devotion to racist pseudoscientific mysticism about the belief that the race not stricken by the plague was "destined by evolution" to be the superior race and inherit that planet, and that he can't interfere with that process.

It's an episode that draws heavily from discredited 19th and early 20th century conceptions of racial Social Darwinism and Eugenics. If the writers had bothered to do an hour's worth of internet research, they'd understand how wrong their understanding of evolution was.

The idea was also to show the "wisdom" of the Prime Directive before it was put in place, but it failed utterly on that, too.

The only time I ever saw it was when it premiered. I don't remember anything about it, other than I seem to think favorably about it. Of course, it's possible that was due solely to Billingsley performance and not the content.

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That's pretty much it, Billingsley delivers a solid performance in it and it's a pretty good character piece about Phlox.

In the Pale Moonlight is a very good episode, but its ethics are wrong on more than the "means justify the ends" angle they went with: said "ends" aren't so noble to begin with.
I mean, sure, as viewers, we can agree that Romulan involvement in the war was in everyone's interests and Sisko is clearly convinced of it as well... but if you examine it critically, is it so obvious? And even if it is, who's Sisko to forego the Romulan right to self-determination?

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If the other Alpha Quadrant powers fall, the Romulans essentially lose that right to self-determination. Becoming a Dominion pawn much like the Cardassians did.

They even saw the writing on the wall but allowed distrust to color their judgement.

To me there are a few TOS episodes. Omega Glory comes to mind. The savage "Yangs" (who are white) that love freedom and the "Kohms" (of Asian descent) are oppressed. Great racist undertones and symbolism Roddenberry (as I think he wrote this one).
There are some others like Patterns of Force that seem to play as a joke on the Nazi manifesto. Others were Kirk "frees" a society by destroying their leader (the Apple for example). The message in the latter seems to be "to be happy one must be free" overlooking the fact that what humans consider "happy" or "free" is not what other races or aliens might agree.

"They'll never let you command a ship in this condition!" (In female body)
"She couldn't be happy being...only a woman."

There was also that one with Zefram Cochrane where they determined the entity was female by its 'feminine' behavior patterns, to which Cochrane was horrified. That was just plain stupid.

Also, TNG - The Host. DS9 made the Trill into an equal relationship between host and symbiant, but in The Host is was blatantly slavery.

In The Pale Moonlight is an interesting conversation. By Star Trek morality it's obviously wrong. But it also saved about a trillion lives and preserved the entire Federation way of life.

If you found out tomorrow that the Pearl Harbor attack was actually carried out by England in order to get the US into the war, how would you feel about that? (What if you were Jewish?)

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Well the Host/DS9 Trill dependency is usually explained away by Riker not being Trill and therefore can't fully bond with the symbiont.

As for your Pearl Harbor scenario? As incredible a false flag operation as that would've been, my first response would be I'd want to go after the people who did that. That WW2 beat Nazi Germany, Fascist Italy and Imperial Japan is rather moot if it was British duplicity who killed over 2000 Americans and led the US to war. I'm sure if the Romulans ever found out the Federation assassinated Vreenak they'd go to war for sure. That makes them responsible, at least in part, for every Romulan who died in that war.

Is it a means justify the ends scenario? Sure... that doesn't mean there won't be hell to pay if it's ever uncovered.

For one of my personal most "wrong" episodes, is For the Uniform in Deep Space 9. To summarize

Sisko: I'm pissed! Eddington embarrassed me!

Dax: Oh my, Eddington just announced he has WMDs, and he threatened to use them on Cardassian colonies!

Sisko: WHAT? We better go after him!

*Some time passes*

Eddington: See Captain, just leave the Marquis alone, you're coming after me because I hurt your feelings. You're being like this antagonist in this book I enjoy.

Sisko: Oh, I know how to catch Eddington. I'll be the bad guy! Worf! Prepare a WMD for a Maquis colony!

Whole Crew: Eh, Captain....aren't you a bit out of con-

Sisko: Shut up and fire!

*Maquis colony is just gassed by a Starfleet officer*

Eddington: Jeez, I'm supposed to be the terrorist Maquis, you're the Starfleet officer, who's supposed to uphold the morals of the Federation. Didn't you just have Worf almost extradited to the Klingons after he was accused of blowing up a civilian ship during the heat of battle?

Worf: Yeah, something about losing battles and even our lives to keep innocent civilian lives out of harm, rig-

Sisko: The continuity levels for this episode have been reached by having a Maquis plot! Now surrender, or we'll keep doing this.

Eddington: Sigh, fine. You win.

*Back on DS9*

Dax: You didn't get approval for your whole gassing a colony plan, did you?